Epitaxial growth of material on a lattice-mismatched substrate typically results in a large number of defects due to misfit dislocations and threading dislocations that can greatly reduce performance. Typically, one can reduce the number of defects through continued growth and thermal annealing, thereby forming a buffer layer on which a desired structure of high material quality is grown on. However, several applications require the removal of the defective regions of the buffer layer while protecting the desired structure, even if the buffer material and the structure are composed of the same or similar materials. Existing methods for removal of the buffer layer tend to undesirably damage the desired structure, so it would be an advance in the art to provide suitably improved fabrication methods.